Macs in Chemistry

Insanely Great Science

crystallography

ISOLDE updated

 

ISOLDE 1.2.0 is available, and ready to install for @UCSFChimeraX 1.2! As usual, just get the ChimeraX 1.2 release from https://www.rbvi.ucsf.edu/chimerax/download.html then install ISOLDE via "Tools/More Tools. Code is on GitHub https://github.com/tristanic/isolde.

ISOLDE is a plugin to UCSF ChimeraX, designed to ease the task of macromolecular model building into low-to-medium resolution maps derived from crystallographic or electron cryo-microscopy (cryoEM) experiments.

UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX can be downloaded free of charge for academic, government, nonprofit, and personal use.

You can view snapshot here https://twitter.com/CrollTristan/status/1390709520876331009

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CSD Software Portfolio from the CCDC upgraded for Big Sur

 

The full CSD software portfolio, including Mercury, ConQuest, Mogul, GOLD, CSD-CrossMiner, the CSD Python API and other components, has now been upgraded and tested for compatibility with Big Sur. We are pleased to report that the newly available 2020.3.1 CSD Release (only available on macOS) is fully supported on macOS Big Sur at point of release, both for Intel-based macs, as well as the newer M1 Apple silicon based macs. At this point we are aware of just two specific known issues for the newer silicon hardware machines:

  • The POV-Ray integration in Mercury for high-resolution graphics generation does not work on M1 Apple silicon based macs
  • The Aromatics Analyser component in the CSD-Materials menu of Mercury does not work on M1 Apple silicon based macs We expect that these final remaining issues will be addressed in the next CSD software release.

Full details are here https://www.ccdc.cam.ac.uk/solutions/whats-new/.

More details on scientific applications under Big Sur are here https://www.macinchem.org/blog/files/1fd84c61d3f91608c1b9c413c8064cd4-2692.php

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CrystalMaker Software on Apple Silicon

 

CrystalMaker Software Ltd are pleased to confirm that as of today, all our Mac software runs natively on “Apple Silicon” (as well as older, Intel-based Macs) - i.e., they are “Universal Binaries”.

• CrystalMaker 10.6 for Mac: an award-winning program for building, visualizing and understanding all kinds of crystal & molecular structures (and the only real, genuine, native Mac program for crystal structures).

• CrystalDiffract 10.9 for Mac: x-ray and neutron powder diffraction made easy.

• SingleCrystal 4.1 for Mac: the latest iteration of our Apple Design Award-winning program for simulating single-crystal diffraction, auto-indexing observed TEM diffraction patterns, and working with stereographic projections of planes and vectors.

Learn more by visiting their website at: http://crystalmaker.com.


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SingleCrystal 4 Launched

 

CrystalMaker Software Ltd have just announced the release of SingleCrystal 4, this is a complete rewrite of thr Apple Design Award winning software in Objective-C, resulting in a state-of-the-art multi-core, multi-touch, multi-structure program. It’s 100% native Mac code - no emulation; no translators - and hence delivers a seamless Mac 64-bit experience with Retina graphics, multi-touch control, haptic feedback, Finder thumbnails, Quick Look previews, Full Screen Mode, Dark Mode and a dedicated Touch Bar interface for MacBook Pro.

The new Live Intensity Mode lets users edit a crystalline material at the atomic level in real time (moving atoms, changing site occupancies, rotating structural groups) - and immediately see the simulated single-crystal diffraction pattern update.

autoindexing

The software is sold directly by CrystalMaker Software Ltd (http://crystalmaker.com/crystalmaker). Multi-user, education and student licensing options are available.

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CCP4 7.1 Released

 

Just got this message

The CCP4 Core Group is very pleased to announce the release of the latest version of the CCP4 Software Suite. Version 7.1 (Skipton) is now available from the CCP4 download website. The release is available for all Windows, Linux and Mac OSX platforms.

This update includes

COOT 0.9. The latest version of Interactive Model Building Software from Dr. Paul Emsley, MRC/LMB, Cambridge, with many improvements and new features. Currently available only for Mac OSX and Linux users.

CCP4 7.1 represents the final state of 7.0 update series, complemented with newest versions of many important components.

Including new packages such as CCP4 Cloud. A framework for distributed CCP4 Computation

The release notes are here.

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Cambridge Structural Database 2019

 

Cambridge Crystallographic Data Centre (CCDC) announced the first release of CSD data and software update of 2019.

The 2019 CSD Release contains 957,868 unique structures and 973,630 entries (CSD version 5.40) – an increase of more than 57,000 entries. We are currently on course to reach a million structures by summer 2019.

The update includes an exciting new polyhedra display option in our visualisation software Mercury.

Read more here….


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CrystalMaker 10.4

 

The much-awaited CrystalMaker 10.4 is now shipping - complete with full “Dark Mode”.

CrystalMaker and CrystalDiffract are real 64-bit Mac programs, written in Cocoa/Objective-C, with beautiful real Mac interfaces. They’re not Windows or Unix applications reskinned via Qt, Java, wxWidgets they’re the real deal: 100% pure Mac. Thus they are able to offer:-

  • Retina display
  • Multi-touch
  • Force touch
  • Haptic feedback
  • Touch bar interface (MacBook Pro)
  • Dark Mode
  • Full-screen mode and Spaces
  • Quick Look
  • Finder thumbnails
  • QuickTime video
  • Apple Help
  • Code-signed, sandboxed, with “hardened runtime” for maximum security

CrystalMaker 10.4 has over 60 new features, of which the most-important are probably:-

  1. Dark Mode
  2. Sleek new structures library with integrated CrystalViewer (1,100 structures; fully customizable)
  3. New energy-modelling engine: makes designing your own molecules quick and easy, with vibrational spectra simulation.
  4. Live powder diffraction: link CrystalMaker 10.4 with CrystalDiffract 6.8 so that editing a crystal in CrystalMaker automatically updates its simulated powder diffraction pattern in CrystalDiffract.
  5. Interpolate Structures command - makes animating structural behaviour smooth and seamless.
  6. Customizable Atoms Inspector and coordinates display.
  7. Spring-loaded sidebars: move the mouse to the edge of the screen to show the relevant sidebar (works great in full-screen mode).
  8. Powerful video sizing/compression options.
  9. Fat sticks display option (great for emphasising structural channels).
  10. Advanced control over axial vectors with scaling, fonts, positioning, inset etc.

More details are available from the download page http://crystalmaker.com/crystalmaker/

They also have a set of video tutorials available.

CrystalMaker X lets you import data from over 40 different formats: with instant display and powerful customization. CrystalMaker can handle including multi-structure files such as DL_POLY HISTORY - use CrystalMaker's synchronization and animation capabilities to rapidly understand structural behaviour, lattice dynamics, or visualize the trajectory of a simulation. CrystalMaker X can also handle truly massive structures. Take advantage of our unique "Depth Profiling" tool, to rapidly scan ares of interest in massive structures - ideal for characterizing the results from computer models.



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CCP4 release 7.0 update 056 now available

 

Collaborative Computational Project No. 4 (CCP4) exists to produce and support a world-leading, integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques.

Details of the latest update are here https://twitter.com/ccp4_mx/status/991256632729403392


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Collaborative Computational Project No. 4 for Macromolecular X-Ray Crystallography

 

CCP4 exists to produce and support a world-leading, integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques.

update 047 is out and contains updates to:

Component Description Mac OS 64-bit Linux 32-bit Linux 64-bit Windows 32-bit Windows 64-bit
panddas update to 2.11 yes yes yes - -
Molrep PFMOD correction yes yes yes yes yes
pointless 1.11.6 yes yes yes yes yes
pointless1.11.5 bug fix for multi lattice data yes yes yes yes yes
ccp4i2 fixes in molrep interface yes yes yes yes yes
edstats new version yes yes yes yes yes
ccp4i lorestr: fix for interface yes yes yes yes yes
monomers add 0WD,2Q5,6G6,6ZL,79F,7K9,8LL, 9Q8,FJI,OMZ,QUJ,QVE,RU2,YY9 yes yes yes yes yes
monomers Format fix: CPN,CPO,DEF,GCR,IMF,QPT yes yes yes yes yes
monomers Replace: UAP yes yes yes yes yes
ccp4mg fixes bug which causes MG/MrBUMP to not work for many sequences yes yes yes yes yes
ccp4mg update for https access to PDBe yes yes yes yes yes
mmdb2 False "duplicate sequence number" error in case of short residue names yes yes yes yes yes
numpy update to 1.12.1 yes yes yes - -
scipy update to 1.16.1 yes yes yes - -

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OpenEye announces the release of AFITT v2.4.1.

 

AFITT is a crystallographic tool for correctly placing small molecules in real-space density. AFITT merges OpenEye’s Shape and MMFF technologies into a new combined forcefield that fits small molecules into crystallographic density while maintaining excellent chemistry.

Support has been added for Ubuntu 16, OSX 10.10, OSX 10.11, and OSX 10.12. OSX 10.7, OSX 10.8, OSX 10.9, SuSe 11, and Redhat 5 x86 are no longer supported

This release adds support for Coot 0.8. Coot 0.6 and earlier versions are no longer supported.

FLYNN (the ligand fitting application) comes bundled with a refinement dictionary writer, WRITEDICT, that uses the MMFF94 force field to derive geometrical constraints for input ligands or protein-ligand complexes. The output dictionaries enforce, as closely as possible, the input ligand’s geometries while allowing the refinement programs to modify the geometry as needed. This version corrects a serious error in which WRITEDICT wrote incorrect bonds lengths for 5-5, 5-6 heterocycle ring systems. A bug that caused PDB remark data that was more than 72 characters long to be clipped from the refined output has been fixed. This only occured when the input and output file formats were both PDB.


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USPEX Universal Structure Predictor

 

I've added USPEX Universal Structure Predictor: Evolutionary Xtallography to the alphabetical listing of applications

A.R. Oganov, J.C. Schon, M. Jansen, S.M. Woodley, W.W. Tipton, and R.G. Hennig. Appendix: First Blind Test of Inorganic Crystal Structure Prediction Methods, pages 223–231. Wiley-VCH Verlag GmbH & Co. KGaA, 2010.


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CrystalMaker Updates

 

The suite of software to support crystallography has been updated

CrystalDiffract brings the world of x-ray & neutron powder diffraction to your computer.

CrystalMaker is the easiest way to build, visualize and understand structures of crystals and molecules

CrystalViewer a free viewer offers high-quality graphics, plus distance and measurement tools, multi-touch control (Mac) and the ability to view crystal lattices along specific lattice vectors or plane normals. 3D Printing Support - save any displayed structure as an STL file, as supported by most 3D printers.

visualization-link


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CCP4 released

 

The current version is CCP4 7.0 (07 January 2016). The new packages include:
SHELX suite: co distribution for academic users
CCP4I2: new ccp4 interface
DIALS: data processing and integration
ARCIMBOLDO-LITE: molecular replacement pipeline
The updated packages include PHASER, XIA2, REFMAC, MONOMER LIBRARY, AMPLE, COOT, AIMLESS POINTLESS, CTRUNCATE, DIMPLE, BLEND and many more

CCP4 exists to produce and support a world-leading, integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques.

The latest version supports Mac OSX and Linux and requires X11. Source code is also available.

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Mac OSX installer for Coot

 

A reader sent me a link to a posting on the brilliant Crystallography on OS X website highlighting the availability of a stand alone version of Coot for Mac OSX

With considerable help from Nat Echols, we can now build coot automatically every night a new revision is available. I have two versions, built on two different computers. The 10.6 version should run on 10.6.8 or greater. The 10.9 version is for 10.9 or later.. The package installer will install everything in /Library/Coot. Unfortunately, it breaks if you move it. A wrapper shell script called "coot" will reside in /usr/local/bin/coot when you are done.

Coot (Crystallographic Object-Oriented Toolkit) is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data.

Coot displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots, skeletonization, non-crystallographic symmetry and more.

I've also added a link on the Spectroscopy page.

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DiffPy

 

DiffPy - Atomic Structure Analysis in Python A free and open source software project to provide python software for diffraction analysis and the study of the atomic structure of materials.

diffpy

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EnCIFer for CIF validation

 

The Crystallographic Information File (CIF) is the internationally agreed standard file format for information exchange in crystallography. The CIF standard is supported, maintained and developed by the International Union of Crystallography (IUCr) and most major journals require electronic data depositions in CIF format. enCIFer enables users to validate CIFs and ensure their files are format-compliant for deposition with journals and databases or for storage in laboratory archives. enCIFer should also be used to add information safely to CIFs without corrupting the strict syntax. enCIFer operates on single or multi-block CIFs allowing you to:

  • Identify and correct syntax/format violations
  • Safely edit information to your CIF without corrupting the strict syntax, for both single data items and data loops
  • Supplement the data in your CIF via two data entry wizards, one for publication details and the other for chemical, physical and crystallographic properties
  • Select from a choice of CIF dictionaries and check against a user-customisable list of mandatory data items
  • Visualise structure(s) in a CIF, including displacement ellipsoids

Requires Mac OS X: 10.6, 10.7, 10.8, 10.9

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AFITT v2.3 has been released

AFITT v2.3 has been released

AFITT merges OpenEye’s Shape and MMFF technologies into a new combined forcefield that fits small molecules into crystallographic density while maintaining excellent chemistry. The AFITT GUI also provides an interface to external refinement programs and tools to validate the refinement including interactive Ramachandran plots and real-space correlation coefficient calculation.

ENHANCEMENTS:

  • PM3/AM1 semi-empirical quantum force field support
  • Better density detection, especially for poor ligand density
  • Optimization enhancements for high-strain ligands
  • (AFITT-GUI) – Protein side-chain fitting (not enabled by default)
  • (AFITT-GUI) – Hydrogen bond visualization (on by default)
  • (AFITT-GUI) – Conflicts with default dictionaries (CCP4) visualized
  • (AFITT-GUI) – Speed improvements in wizard navigation
  • (AFITT-CL) – More control on report and logging generation